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- EMDB-17583: CHAPSO treated partial catalytic component (comprising only AnfD ... -

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Basic information

Entry
Database: EMDB / ID: EMD-17583
TitleCHAPSO treated partial catalytic component (comprising only AnfD & AnfK, lacking AnfG and FeFeco) of iron nitrogenase from Rhodobacter capsulatus
Map dataCore complex of Fe-nitrogenase comprising only AnfD and AnfK.
Sample
  • Complex: CHAPSO treated partial catalytic component (comprising only AnfD & AnfK, lacking AnfG and FeFeco) of iron nitrogenase from Rhodobacter capsulatus
    • Protein or peptide: Nitrogenase protein alpha chain
    • Protein or peptide: Nitrogenase iron-iron protein, beta subunit
  • Ligand: FE(8)-S(7) CLUSTER
Keywordsnitrogen fixation / Fe nitrogenase / OXIDOREDUCTASE
Function / homology
Function and homology information


nitrogenase / carbonyl sulfide nitrogenase activity / nitrogenase activity / nitrogen fixation / iron-sulfur cluster binding / ATP binding / metal ion binding
Similarity search - Function
Nitrogenase iron-iron protein, alpha chain / Nitrogenase iron-iron, beta subunit / Nitrogenase alpha chain / Nitrogenase component 1, alpha chain / Nitrogenase component 1, conserved site / Nitrogenases component 1 alpha and beta subunits signature 2. / Nitrogenases component 1 alpha and beta subunits signature 1. / Nitrogenase/oxidoreductase, component 1 / Nitrogenase component 1 type Oxidoreductase
Similarity search - Domain/homology
Nitrogenase protein alpha chain / Nitrogenase iron-iron protein, beta subunit
Similarity search - Component
Biological speciesRhodobacter capsulatus SB 1003 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.49 Å
AuthorsSchmidt FV / Schulz L / Zarzycki J / Prinz S / Erb TJ / Rebelein JG
Funding support Germany, 2 items
OrganizationGrant numberCountry
Max Planck Society Germany
German Research Foundation (DFG)446841743 Germany
CitationJournal: Nat Struct Mol Biol / Year: 2024
Title: Structural insights into the iron nitrogenase complex.
Authors: Frederik V Schmidt / Luca Schulz / Jan Zarzycki / Simone Prinz / Niels N Oehlmann / Tobias J Erb / Johannes G Rebelein /
Abstract: Nitrogenases are best known for catalyzing the reduction of dinitrogen to ammonia at a complex metallic cofactor. Recently, nitrogenases were shown to reduce carbon dioxide (CO) and carbon monoxide ...Nitrogenases are best known for catalyzing the reduction of dinitrogen to ammonia at a complex metallic cofactor. Recently, nitrogenases were shown to reduce carbon dioxide (CO) and carbon monoxide to hydrocarbons, offering a pathway to recycle carbon waste into hydrocarbon products. Among the three nitrogenase isozymes, the iron nitrogenase has the highest wild-type activity for the reduction of CO, but the molecular architecture facilitating these activities has remained unknown. Here, we report a 2.35-Å cryogenic electron microscopy structure of the ADP·AlF-stabilized iron nitrogenase complex from Rhodobacter capsulatus, revealing an [FeSC-(R)-homocitrate] cluster in the active site. The enzyme complex suggests that the iron nitrogenase G subunit is involved in cluster stabilization and substrate channeling and confers specificity between nitrogenase reductase and catalytic component proteins. Moreover, the structure highlights a different interface between the two catalytic halves of the iron and the molybdenum nitrogenase, potentially influencing the intrasubunit 'communication' and thus the nitrogenase mechanism.
History
DepositionJun 9, 2023-
Header (metadata) releaseOct 4, 2023-
Map releaseOct 4, 2023-
UpdateJan 31, 2024-
Current statusJan 31, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17583.png

Downloads & links

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Map

FileDownload / File: emd_17583.map.gz / Format: CCP4 / Size: 129.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCore complex of Fe-nitrogenase comprising only AnfD and AnfK.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 324 pix.
= 271.188 Å		0.84 Å/pix.
x 324 pix.
= 271.188 Å		0.84 Å/pix.
x 324 pix.
= 271.188 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.837 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-1.9182928 - 2.764598
Average (Standard dev.)-0.00071017485 (±0.06819372)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions324324324
Spacing324324324
CellA=B=C: 271.18802 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half-map A

Fileemd_17583_half_map_1.map
Annotationhalf-map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half-map B

Fileemd_17583_half_map_2.map
Annotationhalf-map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : CHAPSO treated partial catalytic component (comprising only AnfD ...

EntireName: CHAPSO treated partial catalytic component (comprising only AnfD & AnfK, lacking AnfG and FeFeco) of iron nitrogenase from Rhodobacter capsulatus
Components
  • Complex: CHAPSO treated partial catalytic component (comprising only AnfD & AnfK, lacking AnfG and FeFeco) of iron nitrogenase from Rhodobacter capsulatus
    • Protein or peptide: Nitrogenase protein alpha chain
    • Protein or peptide: Nitrogenase iron-iron protein, beta subunit
  • Ligand: FE(8)-S(7) CLUSTER

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Supramolecule #1: CHAPSO treated partial catalytic component (comprising only AnfD ...

SupramoleculeName: CHAPSO treated partial catalytic component (comprising only AnfD & AnfK, lacking AnfG and FeFeco) of iron nitrogenase from Rhodobacter capsulatus
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Rhodobacter capsulatus SB 1003 (bacteria)

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Macromolecule #1: Nitrogenase protein alpha chain

MacromoleculeName: Nitrogenase protein alpha chain / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rhodobacter capsulatus SB 1003 (bacteria)
Molecular weightTheoretical: 60.221117 KDa
Recombinant expressionOrganism: Rhodobacter capsulatus SB 1003 (bacteria)
SequenceString: MPYHEFEVSK CIPERREHAV MKAAGEDLTS CLPKGYLNTI PGTISERGCA YCGAKHVIGT PMKDVIHISH GPNGCTYDTW QTKRYISDN DNFQLKYTFA TDVKEKHVVF GAEGLLKKSM HEAFDAFPNI KRMTVYQTCT TALIGDDVDA IAKEVMEERG D VDVFVCNS ...String:
MPYHEFEVSK CIPERREHAV MKAAGEDLTS CLPKGYLNTI PGTISERGCA YCGAKHVIGT PMKDVIHISH GPNGCTYDTW QTKRYISDN DNFQLKYTFA TDVKEKHVVF GAEGLLKKSM HEAFDAFPNI KRMTVYQTCT TALIGDDVDA IAKEVMEERG D VDVFVCNS PGFAGPSQSG GHHKINIAWL NQKVGTVEPD YLGEHVINYV GEYNIQGDQE VMIDYFNRMG IQVLSTFTGN GS YDSLRMM HRAHLNVLEC ARSAEYICDE LRARYGIPRL DIDGFGFEPL ANSLRKVALF FGIEDKAEAI IAEEYAKWKP QLD WYKERL KGKKVCLWPG GSKLWHWAHA IEEEMGLKVV SVYTKFGHQG DMEKGVSRCG EGALAIDDPN ELESVEAIEM LKPD IIFTG KRPGEFVKKH GVPYLNAHAY HNGPYKGFEG WVRFARDIYN AIYSPMRQLA ALDISAPDAA ITSGFRTAKM NADLT VSDE VKFSEVLHEY TGKYDSIAEI RARNQAYAAE QKALRDAVQP AAEWSHPQFE K

UniProtKB: Nitrogenase protein alpha chain

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Macromolecule #2: Nitrogenase iron-iron protein, beta subunit

MacromoleculeName: Nitrogenase iron-iron protein, beta subunit / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: nitrogenase
Source (natural)Organism: Rhodobacter capsulatus SB 1003 (bacteria)
Molecular weightTheoretical: 50.776398 KDa
Recombinant expressionOrganism: Rhodobacter capsulatus SB 1003 (bacteria)
SequenceString: MTCQVTQKAR EGTINPIFTC QPAGAQFASI GIKDCIGIVH GGQGCVMFVR LLISQHMKES FEIASSSVHE DGAVFGALDR VETAVEVLL TRYPDVKVVP IITTCSTEII GDDVDGLLSK LEDELLPTKF PGREVHLLTV HCPSFVGSMI TGYDKAVHDF V KKFATKDE ...String:
MTCQVTQKAR EGTINPIFTC QPAGAQFASI GIKDCIGIVH GGQGCVMFVR LLISQHMKES FEIASSSVHE DGAVFGALDR VETAVEVLL TRYPDVKVVP IITTCSTEII GDDVDGLLSK LEDELLPTKF PGREVHLLTV HCPSFVGSMI TGYDKAVHDF V KKFATKDE PSDKINLITG WVNPGDVKEL KHLLEVMEVK ANVLFEVESF DSPLMPDLEH HSHGSTTIED LRDTANAKGT IA LNRYEGM KAADYLKKKF KVPAVIGPTP VGIRNTDAFL KAVSEMTGQP IPAQLVKERG LALDAIADIG HMFLADKRVA IYA NPDLAI GLTEFCLDLE MKPKLLLLGD DNSGYVKDPR VLALQENAPD LEIVTNADFW DLESRIQQGL ELDLILGHSK GRFI SIDYK VPMVRVGFPT YDRAGMYRHP VLGYGGAMFL AETMANTLFA DMEAKKNKEW ILNVW

UniProtKB: Nitrogenase iron-iron protein, beta subunit

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Macromolecule #3: FE(8)-S(7) CLUSTER

MacromoleculeName: FE(8)-S(7) CLUSTER / type: ligand / ID: 3 / Number of copies: 2 / Formula: CLF
Molecular weightTheoretical: 671.215 Da
Chemical component information

ChemComp-CLF:
FE(8)-S(7) CLUSTER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.75 mg/mL
BufferpH: 7.8
Details: 37.5 mM TRIS (pH = 7.8) 150 mM NaCl 3.75 mM sodium dithionite 0.4 % (m/V) CHAPSO
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 90 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.4000000000000001 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 7962489
Startup modelType of model: INSILICO MODEL
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. 4.1.1)
Final 3D classificationNumber classes: 10 / Avg.num./class: 130000 / Software - Name: cryoSPARC (ver. 4.1.1)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. 4.1.1)
Final reconstructionNumber classes used: 7 / Applied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.49 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.1.1) / Number images used: 927406
FSC plot (resolution estimation)

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